scholarly journals probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity

2008 ◽  
Vol 10 (10) ◽  
pp. 2894-2898 ◽  
Author(s):  
Alexander Loy ◽  
Roland Arnold ◽  
Patrick Tischler ◽  
Thomas Rattei ◽  
Michael Wagner ◽  
...  
1998 ◽  
Vol 37 (4-5) ◽  
pp. 303-306 ◽  
Author(s):  
R. Howarth ◽  
I. M. Head ◽  
R. F. Unz

Nearly complete 16S ribosomal RNA (rRNA) sequences were determined for fully characterised axenic strains of Thiothrix, Eikelboom type O21N, and Eikelboom type 1701 originally isolated from bulking activated sludges. Thiothrix strains formed a monophyletic group (100% bootstrap support) with previously described Thiothrix nivea strain JP2 and Thiothrix ramosa. Eikelboom type O21N strain AP3 revealed a sufficiently strong relationship to the Thiothrix group to suggest a common ancestry for the two organism although it was not possible to designate type 021N as a species of Thiothrix. Eikelboom type 1701 contained within its sequence the target sequence of an oligonucleotide probe for the detection of Sphaerotilus natans.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Valérie Andrieu-Ponel ◽  
Pierre Rochette ◽  
François Demory ◽  
Hülya Alçiçek ◽  
Nicolas Boulbes ◽  
...  

AbstractCereals are a central resource for the human diet and are traditionally assumed to have evolved from wild grasses at the onset of the Neolithic under the pressure of agriculture. Here we demonstrate that cereals may have a significantly longer and more diverse lineage, based on the study of a 0–2.3 Ma, 601 m long sedimentary core from Lake Acıgöl (South-West Anatolia). Pollen characteristic of cereals is abundant throughout the sedimentary sequence. The presence of large lakes within this arid bioclimatic zone led to the concentration of large herbivore herds, as indicated by the continuous occurrence of coprophilous fungi spores in the record. Our hypothesis is that the effects of overgrazing on soils and herbaceous stratum, during this long period, led to genetic modifications of the Poaceae taxa and to the appearance of proto-cereals. The simultaneous presence of hominins is attested as early as about 1.4 Ma in the lake vicinity, and 1.8 Ma in Georgia and Levant. These ancient hominins probably benefited from the availability of these proto-cereals, rich in nutrients, as well as various other edible plants, opening the way, in this region of the Middle East, to a process of domestication, which reached its full development during the Neolithic.


1988 ◽  
Vol 79 (2) ◽  
pp. 190-192 ◽  
Author(s):  
C. Meisen ◽  
M. Higuchi ◽  
S. Br�utigam ◽  
A. J. Driesel ◽  
M. Blandfort ◽  
...  

1995 ◽  
Vol 41 (1) ◽  
pp. 75-87 ◽  
Author(s):  
Zerlina M. Naczynski ◽  
Andrew M. Kropinski ◽  
Chris Mueller

A 31 base pair synthetic oligonucleotide based on the genes for the Escherichia coli heat shock sigma factor (rpoH) and the Pseudomonas aeruginosa housekeeping sigma factor (rpoD) was employed in conjunction with the Tanaka et al. (K. Tanaka, T. Shiina, and H. Takahashi, 1988. Science (Washington, D.C.), 242: 1040–1042) RpoD box probe to identify the location of the rpoH gene in P. aeruginosa genomic digests. This gene was cloned into plasmid pGEM3Z(f+), sequenced, and found to share 67% nucleotide identity and 77% amino acid homology with the rpoH gene and its product (σ32) of E. coli. The plasmid containing the rpoH gene complemented the function of σ32 in an E. coli rpoH deletion mutant. Furthermore, this plasmid directed the synthesis of a 32-kDa protein in an E. coli S-30 in vitro transcription–translation system. Primer extension studies were used to identify the transcriptional start sites under control and heat-stressed (45 and 50 °C) conditions. Two promoter sites were identified having sequence homology to the E. coli σ70 and σ24 consensus sequences.Key words: heat shock, Pseudomonas aeruginosa, sigma factor, transcription, oligonucleotide probe.


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